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v2.8.0

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@jougs jougs released this 03 Nov 10:04
v2.8.0
6a55c61

DOI License

NEST 2.8.0 is distributed under the GNU General Public License version 2 (or later). This version marks the completion of our development efforts during the HBP ramp up phase and consists of 290 repository checkins by 25 developers since 2.6.0. The most notable changes are:

  • The new connection framework introduced in NEST 2.6.0 can now handle parameter arrays for the 'all-to-all' and 'one-to-one' rules.
  • A new propagator for integrate-and-fire neurons correctly handles the case where membrane and synapse time constants are similar or the same.
  • Better documentation and much extended examples for PyNEST improve the discoverability of NEST's features.

All users are encouraged to upgrade and adapt their simulation scripts to the changes in the user interface at this point in time to benefit from the improvements in the new version.

Changes of default behavior and functionality

  • Topology functions are now available from the main namespace in SLI.
  • The parameters of sinusoidal_poisson_generator and sinusoidal_gamma_generator were changed as follows:
    • dc -> rate
    • ac -> amplitude
    • freq -> frequency
    • phi -> phase; units changed from radian to degrees
  • The parameter name amplitude of ppd_sup_generator was changed to relative_amplitude.
  • Previously most synapse models prohibited the case of tau_m being equal to tau_syn because of the numerics used. The integrate-and-fire neurons now use a different propagator if tau_syn and tau_m are the same or very similar. This might lead to slightly different membrane potential values in these cases than before. See doc/model_details/IAF_neurons_singularity.ipynb for details

New models and examples

  • spike_dilutor repeats incoming spikes with a certain probability.
  • correllospinmatrix_detector allows to measure the covariance matrix from several inputs.
  • brunel-2000_newconnect.sli demonstrates the use of the new connection framework.
  • brunel-2000_newconnect_dc.sli using DC instead of Poisson stimulation.
  • precise_spiking.py compares precise and grid-constrained neuron model.

Documentation improvements

  • All PyNEST examples are now extensively documented and available from nest-simulator.org.
  • The Potjans_2014 example now has an updated documentation.
  • Topology user manual now explains how to connect devices to subregions of layers.
  • noise generator now has documentation in form of a Jupyter Notebook in doc/model_details/noise_generator.ipynb.
  • The voltmeter is now documented and the documentation of multimeter is fixed.
  • The emit() function in precise models is now properly documented.
  • The online help of cont_delay_synapse now has usage examples.

Bug fixes

  • pp_psc_delta now works correctly with multiple calls to Simulate
  • The membrane potential of izhikevichis now more consistent with the original Matlab implementation.
  • hpc_benchmark.sli now aborts when attempting to run with too few local neurons to record from.

Minor changes

  • SLI can now extract information about their origin in the revision control system.
  • MPI is now initialized with mode THREAD_FUNNELED instead of THREAD_SERIALIZED.
  • Module handling in the build system got simplified and cleaned up.
  • Topology free layers now work for single neuron layers.
  • CreateLayer is up to 100-fold faster for large networks.
  • pp_pop_psc_delta uses a refined check for small spike probability.
  • The logos were updated and are available in extras/logos.
  • The PyNEST testsuite now also runs on older NumPy and Python versions.
  • Rebuilding the NEST build system now requires autoconf >= 2.63.
  • Renovations to MyModule's build system allow to also build modules on BlueGene.
  • The last occurrences of CPEX were removed from the Communicator class.
  • New scripts execute static code analysis and formatting locally as TravisCI would do it.

Testsuite improvements

  • CreateLayer now has a regression test.
  • iaf_cond_alpha_mc and cont_delay_synapse have new unit tests.
  • do_tests.sh now returns non-zero exit code in case of failing tests.

Contributors since v2.6.0

  • Sacha van Albada
  • Claudia Bachmann
  • Hannah Bos
  • Rajalekshmi Deepu
  • Moritz Deger
  • Renato Duarte
  • Jochen M. Eppler
  • Marc-Oliver Gewaltig
  • Espen Hagen
  • Moritz Helias
  • Tammo Ippen
  • Jakob Jordan
  • Susanne Kunkel
  • Frank Michler
  • Abigail Morrison
  • Robin Pauli
  • Alexander Peyser
  • Luis Riquelme
  • Hans Ekkehard Plesser
  • Wolfram Schenk
  • Maximilian Schmidt
  • Jannis Schuecker
  • Johanna Senk
  • Hesam Setareh
  • Ali Shirvani
  • Tiziano Zito

Citation

If you use this version of NEST, please cite it as Eppler, Jochen Martin et al. (2015). NEST 2.8.0. Zenodo. 10.5281/zenodo.32969. The full citation is available in different formats on Zenodo.

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